1
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Cheng J, Zhang K, Hou Y. The current situations and limitations of genetic engineering in cyanobacteria: a mini review. Mol Biol Rep 2023; 50:5481-5487. [PMID: 37119415 DOI: 10.1007/s11033-023-08456-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/12/2023] [Indexed: 05/01/2023]
Abstract
Cyanobacteria are an ancient group of photoautotrophic prokaryotes, and play an essential role in the global carbon cycle. They are also model organisms for studying photosynthesis and circadian regulation, and metabolic engineering and synthetic biology strategies grants light-driven biotechnological applications to cyanobacteria, especially for engineering cyanobacteria cells to achieve an efficient light-driven system for synthesizing any product of interest from renewable feedstocks. However, lower yield limits the potential of industrial application of cyanobacterial synthetic biology, and some key limitations must be overcome to realize the full biotechnological potential of these versatile microorganisms. Although genetic engineering toolkits for cyanobacteria have made some progress, the tools available still lag behind conventional heterotrophic microorganism. Consequently, this study describes the current situations and limitations of genetic engineering in cyanobacteria, and further improvements are proposed to improve the output of targeted products. We believe that cyanobacteria-mediated light-driven platforms towards efficient synthesis of green chemicals could unlock a bright future by developing the tools for strain manipulation and novel chassis organisms with excellent performance for biotechnological applications, which could also accelerate the advancement of bio-manufacturing industries.
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Affiliation(s)
- Jie Cheng
- School of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, 570100, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| | - Yuyong Hou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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2
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Riaz S, Jiang Y, Xiao M, You D, Klepacz-Smółka A, Rasul F, Daroch M. Generation of miniploid cells and improved natural transformation procedure for a model cyanobacterium Synechococcus elongatus PCC 7942. Front Microbiol 2022; 13:959043. [PMID: 35958137 PMCID: PMC9360974 DOI: 10.3389/fmicb.2022.959043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
The biotechnologically important and naturally transformable cyanobacterium, Synechococcus elongatus PCC 7942, possesses multiple genome copies irrespective of its growth rate or condition. Hence, segregating mutations across all genome copies typically takes several weeks. In this study, Synechococcus 7942 cultivation on a solid growth medium was optimised using different concentrations of agar, the addition of antioxidants, and overexpression of the catalase gene to facilitate the rapid acquisition of colonies and fully segregated lines. Synechococcus 7942 was grown at different temperatures and nutritional conditions. The miniploid cells were identified using flow cytometry and fluorimetry. The natural transformation was carried out using miniploid cells and validated with PCR and high performance liquid chromatography (HPLC). We identified that 0.35% agar concentration and 200 IU of catalase could improve the growth of Synechococcus 7942 on a solid growth medium. Furthermore, overexpression of a catalase gene enhanced the growth rate and supported diluted culture to grow on a solid medium. Our results reveal that high temperature and phosphate-depleted cells contain the lowest genome copies (2.4 ± 0.3 and 1.9 ± 0.2) and showed the potential to rapidly produce fully segregated mutants. In addition, higher antibiotic concentrations improve the selection of homozygous transformants while maintaining similar genome copies at a constant temperature. Based on our observation, we have an improved cultivation and natural transformation protocol for Synechococcus 7942 by optimising solid media culturing, generating low-ploidy cells that ultimately reduced the time required for the complete segregation of engineered lines.
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Affiliation(s)
- Sadaf Riaz
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT, United States
| | - Ying Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Meng Xiao
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Dawei You
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Anna Klepacz-Smółka
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, University of Technology, Łódź, Poland
| | - Faiz Rasul
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
- *Correspondence: Maurycy Daroch,
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3
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Mills LA, Moreno-Cabezuelo JÁ, Włodarczyk A, Victoria AJ, Mejías R, Nenninger A, Moxon S, Bombelli P, Selão TT, McCormick AJ, Lea-Smith DJ. Development of a Biotechnology Platform for the Fast-Growing Cyanobacterium Synechococcus sp. PCC 11901. Biomolecules 2022; 12:biom12070872. [PMID: 35883428 PMCID: PMC9313322 DOI: 10.3390/biom12070872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023] Open
Abstract
Synechococcus sp. PCC 11901 reportedly demonstrates the highest, most sustained growth of any known cyanobacterium under optimized conditions. Due to its recent discovery, our knowledge of its biology, including the factors underlying sustained, fast growth, is limited. Furthermore, tools specific for genetic manipulation of PCC 11901 are not established. Here, we demonstrate that PCC 11901 shows faster growth than other model cyanobacteria, including the fast-growing species Synechococcuselongatus UTEX 2973, under optimal growth conditions for UTEX 2973. Comparative genomics between PCC 11901 and Synechocystis sp. PCC 6803 reveal conservation of most metabolic pathways but PCC 11901 has a simplified electron transport chain and reduced light harvesting complex. This may underlie its superior light use, reduced photoinhibition, and higher photosynthetic and respiratory rates. To aid biotechnology applications, we developed a vitamin B12 auxotrophic mutant but were unable to generate unmarked knockouts using two negative selectable markers, suggesting that recombinase- or CRISPR-based approaches may be required for repeated genetic manipulation. Overall, this study establishes PCC 11901 as one of the most promising species currently available for cyanobacterial biotechnology and provides a useful set of bioinformatics tools and strains for advancing this field, in addition to insights into the factors underlying its fast growth phenotype.
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Affiliation(s)
- Lauren A. Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - José Ángel Moreno-Cabezuelo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Artur Włodarczyk
- Bondi Bio Pty Ltd., c/o Climate Change Cluster, University of Technology Sydney, 745 Harris Street, Ultimo, NSW 2007, Australia;
| | - Angelo J. Victoria
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Rebeca Mejías
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Anja Nenninger
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK;
| | - Tiago T. Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
- Correspondence:
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4
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Zieliński T, Hay J, Romanowski A, Nenninger A, McCormick A, Millar AJ. SynBio2Easy-a biologist-friendly tool for batch operations on SBOL designs with Excel inputs. SYNTHETIC BIOLOGY (OXFORD, ENGLAND) 2022; 7:ysac002. [PMID: 35350192 PMCID: PMC8944294 DOI: 10.1093/synbio/ysac002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/26/2021] [Accepted: 01/25/2022] [Indexed: 01/09/2023]
Abstract
Practical delivery of Findable, Accessible, Reusable and Interoperable principles for research data management requires expertise, time resource, (meta)data standards and formats, software tools and public repositories. The Synthetic Biology Open Language (SBOL2) metadata standard enables FAIR sharing of the designs of synthetic biology constructs, notably in the repository of the SynBioHub platform. Large libraries of such constructs are increasingly easy to produce in practice, for example, in DNA foundries. However, manual curation of the equivalent libraries of designs remains cumbersome for a typical lab researcher, creating a barrier to data sharing. Here, we present a simple tool SynBio2Easy, which streamlines and automates operations on multiple Synthetic Biology Open Language (SBOL) designs using Microsoft Excel® tables as metadata inputs. The tool provides several utilities for manipulation of SBOL documents and interaction with SynBioHub: for example, generation of a library of plasmids based on an original design template, bulk deposition into SynBioHub, or annotation of existing SBOL component definitions with notes and authorship information. The tool was used to generate and deposit a collection of 3661 cyanobacterium Synechocystis plasmids into the public SynBioHub repository. In the process of developing the software and uploading these data, we evaluated some aspects of the SynBioHub platform and SBOL ecosystem, and we discuss proposals for improvement that could benefit the user community. With software such as SynBio2Easy, we aim to deliver a user-driven tooling to make FAIR a reality at all stages of the project lifecycle in synthetic biology research. Graphical Abstract.
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Affiliation(s)
- Tomasz Zieliński
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Johnny Hay
- EPCC, University of Edinburgh, Edinburgh, UK
| | - Andrew Romanowski
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Anja Nenninger
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alistair McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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5
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The Molecular Toolset and Techniques Required to Build Cyanobacterial Cell Factories. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022. [DOI: 10.1007/10_2022_210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Jones CM, Parrish S, Nielsen DR. Exploiting Polyploidy for Markerless and Plasmid-Free Genome Engineering in Cyanobacteria. ACS Synth Biol 2021; 10:2371-2382. [PMID: 34530614 DOI: 10.1021/acssynbio.1c00269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we describe a universal approach for plasmid-free genome engineering in cyanobacteria that exploits the polyploidy of their chromosomes as a natural counterselection system. Rather than being delivered via replicating plasmids, genes encoding for DNA modifying enzymes are instead integrated into essential genes on the chromosome by allelic exchange, as facilitated by antibiotic selection, a process that occurs readily and with only minor fitness defects. By virtue of the essentiality of these integration sites, full segregation is never achieved, with the strain instead remaining as a merodiploid so long as antibiotic selection is maintained. As a result, once the desired genome modification is complete, removal of antibiotic selection results in the gene encoding for the DNA modifying enzyme to then be promptly eliminated from the population. Proof of concept of this new and generalizable strategy is provided using two different site-specific recombination systems, CRE-lox and DRE-rox, in the fast-growing cyanobacterium Synechococcus sp. PCC 7002, as well as CRE-lox in the model cyanobacterium Synechocystis sp. PCC 6803. Reusability of the method, meanwhile, is demonstrated by constructing a high-CO2 requiring and markerless Δndh3 Δndh4 ΔbicA ΔsbtA mutant of Synechococcus sp. PCC 7002. Overall, this method enables the simple and efficient construction of stable and unmarked mutants in cyanobacteria without the need to develop additional shuttle vectors nor counterselection systems.
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Affiliation(s)
- Christopher M. Jones
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Sydney Parrish
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
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7
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Chen L, Liu H, Wang L, Tan X, Yang S. Synthetic counter-selection markers and their application in genetic modification of Synechococcus elongatus UTEX2973. Appl Microbiol Biotechnol 2021; 105:5077-5086. [PMID: 34106311 DOI: 10.1007/s00253-021-11391-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/26/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Due to its robustness to environmental stresses and fast growth, Synechococcus elongatus UTEX2973 is developed as a new model for researches on cyanobacterial molecular biology and biotechnology. However, systematic genetic modifications of S. elongatus UTEX2973 were hindered by the lack of effective genetic manipulation tools, especially available counter-selection markers. Here, six synthetic counter-selection markers (SCOMs) were assembled by fusing six toxin genes from either Escherichia coli or cyanobacteria with a theophylline-inducible promoter. The SCOMs containing SYNPCC7002_G0085 from Synechococcus sp. PCC7002 or mazF from E. coli were proved to be inducible by theophylline in S. elongatus UTEX2973. By using the mazF-based SCOM, the neutral locus 1 and 23 small regulatory RNAs were completely deleted from the genome of S. elongatus UTEX2973 after one round of selection with both kanamycin and theophylline. The genetic tools developed in this work will facilitate future researches on molecular genetics and synthetic biology in S. elongatus UTEX2973. KEY POINTS: • Two inducible counter-selection markers are lethal to S. elongatus UTEX2973. • The counter-selection marker benefits the gene targeting in S. elongatus UTEX2973. • Twentry-three small regulatory RNAs were fully deleted via the novel gene targeting method.
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Affiliation(s)
- Liyuan Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Hai Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Li Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Xiaoming Tan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062, China
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8
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The Genome Copy Number of the Thermophilic Cyanobacterium Thermosynechococcus elongatus E542 Is Controlled by Growth Phase and Nutrient Availability. Appl Environ Microbiol 2021; 87:AEM.02993-20. [PMID: 33608293 PMCID: PMC8091003 DOI: 10.1128/aem.02993-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/13/2021] [Indexed: 12/20/2022] Open
Abstract
The present study revealed that the genome copy number (ploidy) status in the thermophilic cyanobacterium Thermosynechococcus E542 is regulated by growth phase and various environmental parameters to give us a window into understanding the role of polyploidy. An increased ploidy level is found to be associated with higher metabolic activity and increased vigor by acting as backup genetic information to compensate for damage to the other chromosomal copies. The recently isolated thermophilic cyanobacterium Thermosynechococcus elongatus PKUAC-SCTE542 (here Thermosynechococcus E542) is a promising strain for fundamental and applied research. Here, we used several improved ploidy estimation approaches, which include quantitative PCR (qPCR), spectrofluorometry, and flow cytometry, to precisely determine the ploidy level in Thermosynechococcus E542 across different growth stages and nutritional and stress conditions. The distribution of genome copies per cell among the populations of Thermosynechococcus E542 was also analyzed. The strain tends to maintain 3 or 4 genome copies per cell in lag phase, early growth phase, or stationary phase under standard conditions. Increased ploidy (5.5 ± 0.3) was observed in exponential phase; hence, the ploidy level is growth phase regulated. Nearly no monoploid cells were detected in all growth phases, and prolonged stationary phase could not yield ploidy levels lower than 3 under standard conditions. During the late growth phase, a significantly higher ploidy level was observed in the presence of bicarbonate (7.6 ± 0.7) and high phosphate (6.9 ± 0.2) at the expense of reduced percentages of di- and triploid cells. Meanwhile, the reduction in phosphates decreased the average ploidy level by increasing the percentages of mono- and diploid cells. In contrast, temperature and antibiotic stresses reduced the percentages of mono-, di-, and triploid cells yet maintained average ploidy. The results indicate a possible causality between growth rate, stress, and genome copy number across the conditions tested, but the exact mechanism is yet to be elucidated. Furthermore, the spectrofluorometric approach presented here is a quick and straightforward ploidy estimation method with reasonable accuracy. IMPORTANCE The present study revealed that the genome copy number (ploidy) status in the thermophilic cyanobacterium Thermosynechococcus E542 is regulated by growth phase and various environmental parameters to give us a window into understanding the role of polyploidy. An increased ploidy level is found to be associated with higher metabolic activity and increased vigor by acting as backup genetic information to compensate for damage to the other chromosomal copies. Several improved ploidy estimation approaches that may upgrade the ploidy estimation procedure for cyanobacteria in the future are presented in this work. Furthermore, the new spectrofluorometric method presented here is a rapid and straightforward method of ploidy estimation with reasonable accuracy compared to other laborious methods.
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9
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Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803. Biosci Rep 2021; 40:222317. [PMID: 32149336 PMCID: PMC7133116 DOI: 10.1042/bsr20193325] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.
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10
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Gale GAR, Wang B, McCormick AJ. Evaluation and Comparison of the Efficiency of Transcription Terminators in Different Cyanobacterial Species. Front Microbiol 2021; 11:624011. [PMID: 33519785 PMCID: PMC7843447 DOI: 10.3389/fmicb.2020.624011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria utilize sunlight to convert carbon dioxide into a wide variety of secondary metabolites and show great potential for green biotechnology applications. Although cyanobacterial synthetic biology is less mature than for other heterotrophic model organisms, there are now a range of molecular tools available to modulate and control gene expression. One area of gene regulation that still lags behind other model organisms is the modulation of gene transcription, particularly transcription termination. A vast number of intrinsic transcription terminators are now available in heterotrophs, but only a small number have been investigated in cyanobacteria. As artificial gene expression systems become larger and more complex, with short stretches of DNA harboring strong promoters and multiple gene expression cassettes, the need to stop transcription efficiently and insulate downstream regions from unwanted interference is becoming more important. In this study, we adapted a dual reporter tool for use with the CyanoGate MoClo Assembly system that can quantify and compare the efficiency of terminator sequences within and between different species. We characterized 34 intrinsic terminators in Escherichia coli, Synechocystis sp. PCC 6803, and Synechococcus elongatus UTEX 2973 and observed significant differences in termination efficiencies. However, we also identified five terminators with termination efficiencies of >96% in all three species, indicating that some terminators can behave consistently in both heterotrophic species and cyanobacteria.
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Affiliation(s)
- Grant A. R. Gale
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alistair J. McCormick
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
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11
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Solymosi D, Nikkanen L, Muth-Pawlak D, Fitzpatrick D, Vasudevan R, Howe CJ, Lea-Smith DJ, Allahverdiyeva Y. Cytochrome c M Decreases Photosynthesis under Photomixotrophy in Synechocystis sp. PCC 6803. PLANT PHYSIOLOGY 2020; 183:700-716. [PMID: 32317358 PMCID: PMC7271781 DOI: 10.1104/pp.20.00284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/23/2020] [Indexed: 05/26/2023]
Abstract
Photomixotrophy is a metabolic state that enables photosynthetic microorganisms to simultaneously perform photosynthesis and metabolism of imported organic carbon substrates. This process is complicated in cyanobacteria, since many, including Synechocystis sp. PCC 6803, conduct photosynthesis and respiration in an interlinked thylakoid membrane electron transport chain. Under photomixotrophy, the cell must therefore tightly regulate electron fluxes from photosynthetic and respiratory complexes. In this study, we demonstrate, via characterization of photosynthetic apparatus and the proteome, that photomixotrophic growth results in a gradual inhibition of QA - reoxidation in wild-type Synechocystis, which largely decreases photosynthesis over 3 d of growth. This process is circumvented by deleting the gene encoding cytochrome c M (CytM), a cryptic c-type heme protein widespread in cyanobacteria. The ΔCytM strain maintained active photosynthesis over the 3-d period, demonstrated by high photosynthetic O2 and CO2 fluxes and effective yields of PSI and PSII. Overall, this resulted in a higher growth rate compared to that of the wild type, which was maintained by accumulation of proteins involved in phosphate and metal uptake, and cofactor biosynthetic enzymes. While the exact role of CytM has not been determined, a mutant deficient in the thylakoid-localized respiratory terminal oxidases and CytM (ΔCox/Cyd/CytM) displayed a phenotype similar to that of ΔCytM under photomixotrophy. This, in combination with other physiological data, and in contrast to a previous hypothesis, suggests that CytM does not transfer electrons to these complexes. In summary, our data suggest that CytM may have a regulatory role in photomixotrophy by modulating the photosynthetic capacity of cells.
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Affiliation(s)
- Daniel Solymosi
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
| | - Lauri Nikkanen
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
| | - Dorota Muth-Pawlak
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
| | - Duncan Fitzpatrick
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
| | - Ravendran Vasudevan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - David J Lea-Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Yagut Allahverdiyeva
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
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12
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Pope MA, Hodge JA, Nixon PJ. An Improved Natural Transformation Protocol for the Cyanobacterium Synechocystis sp. PCC 6803. FRONTIERS IN PLANT SCIENCE 2020; 11:372. [PMID: 32351517 PMCID: PMC7174562 DOI: 10.3389/fpls.2020.00372] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
The naturally transformable cyanobacterium Synechocystis sp. PCC 6803 is a widely used chassis strain for the photosynthetic production of chemicals. However, Synechocystis possesses multiple genome copies per cell which means that segregating mutations across all genome copies can be time-consuming. Here we use flow cytometry in combination with DNA staining to investigate the effect of phosphate deprivation on the genome copy number of the glucose-tolerant GT-P sub-strain of Synechocystis 6803. Like the PCC 6803 wild type strain, the ploidy of GT-P cells grown in BG-11 medium is growth phase dependent with an average genome copy number of 6.05 ± 0.27 in early growth (OD740 = 0.1) decreasing to 2.49 ± 0.11 in late stationary phase (OD740 = 7). We show that a 10-fold reduction in the initial phosphate concentration of the BG-11 growth medium reduces the average genome copy number of GT-P cells from 4.51 ± 0.20 to 2.94 ± 0.13 and increases the proportion of monoploid cells from 0 to 6% after 7 days of growth. In addition, we also show that the DnaA protein, which unusually for bacteria is not required for DNA replication in Synechocystis, plays a role in restoring polyploidy upon subsequent phosphate supplementation. Based on these observations, we have developed an alternative natural transformation protocol involving phosphate depletion that decreases the time required to obtain fully segregated mutants.
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13
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Hitchcock A, Hunter CN, Canniffe DP. Progress and challenges in engineering cyanobacteria as chassis for light-driven biotechnology. Microb Biotechnol 2019; 13:363-367. [PMID: 31880868 PMCID: PMC7017823 DOI: 10.1111/1751-7915.13526] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 11/26/2022] Open
Abstract
Cyanobacteria are prokaryotic phototrophs that, in addition to being excellent model organisms for studying photosynthesis, have tremendous potential for light‐driven synthetic biology and biotechnology. These versatile and resilient microorganisms harness the energy of sunlight to oxidise water, generating chemical energy (ATP) and reductant (NADPH) that can be used to drive sustainable synthesis of high‐value natural products in genetically modified strains. In this commentary article for the Synthetic Microbiology Caucus we discuss the great progress that has been made in engineering cyanobacterial hosts as microbial cell factories for solar‐powered biosynthesis. We focus on some of the main areas where the synthetic biology and metabolic engineering tools in cyanobacteria are not as advanced as those in more widely used heterotrophic chassis, and go on to highlight key improvements that we feel are required to unlock the full power of cyanobacteria for future green biotechnology.
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Affiliation(s)
- Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Daniel P Canniffe
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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14
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Gale GAR, Schiavon Osorio AA, Mills LA, Wang B, Lea-Smith DJ, McCormick AJ. Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology. Microorganisms 2019; 7:E409. [PMID: 31569579 PMCID: PMC6843473 DOI: 10.3390/microorganisms7100409] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Recent advances in synthetic biology and an emerging algal biotechnology market have spurred a prolific increase in the availability of molecular tools for cyanobacterial research. Nevertheless, work to date has focused primarily on only a small subset of model species, which arguably limits fundamental discovery and applied research towards wider commercialisation. Here, we review the requirements for uptake of new strains, including several recently characterised fast-growing species and promising non-model species. Furthermore, we discuss the potential applications of new techniques available for transformation, genetic engineering and regulation, including an up-to-date appraisal of current Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) and CRISPR interference (CRISPRi) research in cyanobacteria. We also provide an overview of several exciting molecular tools that could be ported to cyanobacteria for more advanced metabolic engineering approaches (e.g., genetic circuit design). Lastly, we introduce a forthcoming mutant library for the model species Synechocystis sp. PCC 6803 that promises to provide a further powerful resource for the cyanobacterial research community.
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Affiliation(s)
- Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - Alejandra A Schiavon Osorio
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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15
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Vavitsas K, Crozet P, Vinde MH, Davies F, Lemaire SD, Vickers CE. The Synthetic Biology Toolkit for Photosynthetic Microorganisms. PLANT PHYSIOLOGY 2019; 181:14-27. [PMID: 31262955 PMCID: PMC6716251 DOI: 10.1104/pp.19.00345] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/09/2019] [Indexed: 05/10/2023]
Abstract
Photosynthetic microorganisms offer novel characteristics as synthetic biology chassis, and the toolbox of components and techniques for cyanobacteria and algae is rapidly increasing.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
| | - Pierre Crozet
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226, Centre National de la Recherche Scientifique, Sorbonne Université, 75005 Paris, France
| | - Marcos Hamborg Vinde
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
| | - Fiona Davies
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401
| | - Stéphane D Lemaire
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226, Centre National de la Recherche Scientifique, Sorbonne Université, 75005 Paris, France
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
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16
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Vasudevan R, Gale GAR, Schiavon AA, Puzorjov A, Malin J, Gillespie MD, Vavitsas K, Zulkower V, Wang B, Howe CJ, Lea-Smith DJ, McCormick AJ. CyanoGate: A Modular Cloning Suite for Engineering Cyanobacteria Based on the Plant MoClo Syntax. PLANT PHYSIOLOGY 2019; 180:39-55. [PMID: 30819783 PMCID: PMC6501082 DOI: 10.1104/pp.18.01401] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/16/2019] [Indexed: 05/10/2023]
Abstract
Recent advances in synthetic biology research have been underpinned by an exponential increase in available genomic information and a proliferation of advanced DNA assembly tools. The adoption of plasmid vector assembly standards and parts libraries has greatly enhanced the reproducibility of research and the exchange of parts between different labs and biological systems. However, a standardized modular cloning (MoClo) system is not yet available for cyanobacteria, which lag behind other prokaryotes in synthetic biology despite their huge potential regarding biotechnological applications. By building on the assembly library and syntax of the Plant Golden Gate MoClo kit, we have developed a versatile system called CyanoGate that unites cyanobacteria with plant and algal systems. Here, we describe the generation of a suite of parts and acceptor vectors for making (1) marked/unmarked knock-outs or integrations using an integrative acceptor vector, and (2) transient multigene expression and repression systems using known and previously undescribed replicative vectors. We tested and compared the CyanoGate system in the established model cyanobacterium Synechocystis sp. PCC 6803 and the more recently described fast-growing strain Synechococcus elongatus UTEX 2973. The UTEX 2973 fast-growth phenotype was only evident under specific growth conditions; however, UTEX 2973 accumulated high levels of proteins with strong native or synthetic promoters. The system is publicly available and can be readily expanded to accommodate other standardized MoClo parts to accelerate the development of reliable synthetic biology tools for the cyanobacterial community.
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Affiliation(s)
- Ravendran Vasudevan
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Alejandra A Schiavon
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Anton Puzorjov
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - John Malin
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Michael D Gillespie
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Konstantinos Vavitsas
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
- CSIRO, Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
| | - Valentin Zulkower
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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17
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Ito S, Koyama N, Osanai T. Citrate synthase from Synechocystis is a distinct class of bacterial citrate synthase. Sci Rep 2019; 9:6038. [PMID: 30988396 PMCID: PMC6465352 DOI: 10.1038/s41598-019-42659-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/04/2019] [Indexed: 12/03/2022] Open
Abstract
Citrate synthase (CS, EC 2.3.3.1) catalyses the initial reaction of the tricarboxylic acid (TCA) cycle. Although CSs from heterotrophic bacteria have been extensively studied, cyanobacterial CSs are not well-understood. Cyanobacteria can produce various metabolites from carbon dioxide. Synechocystis sp. PCC 6803 (Synechocystis 6803) is a cyanobacterium used to synthesize metabolites through metabolic engineering techniques. The production of acetyl-CoA-derived metabolites in Synechocystis 6803 has been widely examined. However, the biochemical mechanisms of reactions involving acetyl-CoA in Synechocystis 6803 are poorly understood. We characterised the CS from Synechocystis 6803 (SyCS) and compared its characteristics with other bacterial CSs. SyCS catalysed only the generation of citrate, and did not catalyse the cleavage of citrate. It is suggested that SyCS is not related to the reductive TCA cycle. The substrate affinity and turnover number of SyCS were lower than those of CSs from heterotrophic bacteria. SyCS was activated by MgCl2 and CaCl2, which inhibit various bacterial CSs. SyCS was not inhibited by ATP and NADH; which are typical feedback inhibitors of other bacterial CSs. SyCS was inhibited by phosphoenolpyruvate and activated by ADP, which has not been reported for CSs from heterotrophic bacteria. Thus, SyCS showed unique characteristics, particularly its sensitivity to effectors.
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Affiliation(s)
- Shoki Ito
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Naoto Koyama
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
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18
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Lea-Smith DJ, Ortiz-Suarez ML, Lenn T, Nürnberg DJ, Baers LL, Davey MP, Parolini L, Huber RG, Cotton CAR, Mastroianni G, Bombelli P, Ungerer P, Stevens TJ, Smith AG, Bond PJ, Mullineaux CW, Howe CJ. Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria. PLANT PHYSIOLOGY 2016; 172:1928-1940. [PMID: 27707888 PMCID: PMC5100757 DOI: 10.1104/pp.16.01205] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 exhibit significant phenotypic differences from wild type, including enlarged cell size, reduced growth, and increased division defects. Photosynthetic rates were similar between strains, although a minor reduction in energy transfer between the soluble light harvesting phycobilisome complex and membrane-bound photosystems was observed. Hydrocarbons were shown to accumulate in thylakoid and cytoplasmic membranes. Modeling of membranes suggests these compounds aggregate in the center of the lipid bilayer, potentially promoting membrane flexibility and facilitating curvature. In vivo measurements confirmed that Synechococcus sp. PCC 7002 mutants lacking hydrocarbons exhibit reduced thylakoid membrane curvature compared to wild type. We propose that hydrocarbons may have a role in inducing the flexibility in membranes required for optimal cell division, size, and growth, and efficient association of soluble and membrane bound proteins. The recent identification of C15-C17 alkanes and alkenes in microalgal species suggests hydrocarbons may serve a similar function in a broad range of photosynthetic organisms.
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Affiliation(s)
- David J Lea-Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.);
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.);
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.);
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.);
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.);
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.);
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Maite L Ortiz-Suarez
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Tchern Lenn
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Dennis J Nürnberg
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Laura L Baers
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Matthew P Davey
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Lucia Parolini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Roland G Huber
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Charles A R Cotton
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Giulia Mastroianni
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Petra Ungerer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Tim J Stevens
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Alison G Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Peter J Bond
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Conrad W Mullineaux
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
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